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|
<html>
<head>
<title>
HDF5 Draft Disk-Format Specification
</title>
</head>
<body>
<center><h1>HDF5: Disk Format Implementation</h1></center>
<ol type=I>
<li><a href="#BootBlock">
Disk Format Level 0 - File Signature and Boot Block</a>
<li><a href="#ObjectDir">
Disk Format Level 1 - File Infrastructure</a>
<ol type=A>
<li><a href="#Btrees">
Disk Format Level 1A - B-link Trees</a>
<li><a href="#SymbolTable">
Disk Format Level 1B - Symbol Table</a>
<li><a href="#SymbolTableEntry">
Disk Format Level 1C - Symbol Table Entry</a>
<li><a href="#LocalHeap">
Disk Format Level 1D - Local Heaps</a>
<li><a href="#GlobalHeap">
Disk Format Level 1E - Global Heap</a>
<li><a href="#FreeSpaceIndex">
Disk Format Level 1F - Free-Space Index</a>
</ol>
<li><a href="#DataObject">
Disk Format Level 2 - Data Objects</a>
<ol type=A>
<li><a href="#ObjectHeader">
Disk Format Level 2a - Data Object Headers</a>
<ol type=1>
<li><a href="#NILMessage"> <!-- 0x0000 -->
Name: NIL</a>
<li><a href="#SimpleDataSpace"> <!-- 0x0001 -->
Name: Simple Data Space</a>
<li><a href="#DataSpaceMessage"> <!-- 0x0002 -->
Name: Data-Space</a>
<li><a href="#DataTypeMessage"> <!-- 0x0003 -->
Name: Data-Type</a>
<li><a href="#ReservedMessage_0004"> <!-- 0x0004 -->
Name: Reserved - not assigned yet</a>
<li><a href="#ReservedMessage_0005"> <!-- 0x0005 -->
Name: Reserved - not assigned yet</a>
<li><a href="#CompactDataStorageMessage"> <!-- 0x0006 -->
Name: Data Storage - Compact</a>
<li><a href="#ExternalFileListMessage"> <!-- 0x0007 -->
Name: Data Storage - External Data Files</a>
<li><a href="#LayoutMessage"> <!-- 0x0008 -->
Name: Data Storage - Layout</a>
<li><a href="#ReservedMessage_0009"> <!-- 0x0009 -->
Name: Reserved - not assigned yet</a>
<li><a href="#ReservedMessage_000A"> <!-- 0x000a -->
Name: Reserved - not assigned yet</a>
<li><a href="#CompressionMessage"> <!-- 0x000b -->
Name: Data Storage - Compressed</a>
<li><a href="#AttributeListMessage"> <!-- 0x000c -->
Name: Attribute List</a>
<li><a href="#NameMessage"> <!-- 0x000d -->
Name: Object Name</a>
<li><a href="#ModifiedMessage"> <!-- 0x000e -->
Name: Object Modification Date & Time</a>
<li><a href="#SharedMessage"> <!-- 0x000f -->
Name: Shared Object Message</a>
<li><a href="#ContinuationMessage"> <!-- 0x0010 -->
Name: Object Header Continuation</a>
<li><a href="#SymbolTableMessage"> <!-- 0x0011 -->
Name: Symbol Table Message</a>
</ol>
<li><a href="#SharedObjectHeader">
Disk Format: Level 2b - Shared Data Object Headers</a>
<li><a href="#DataStorage">
Disk Format: Level 2c - Data Object Data Storage</a>
</ol>
</ol>
<h2>Disk Format Implementation</h2>
<P>The format of a HDF5 file on disk encompasses several
key ideas of the current HDF4 & AIO file formats as well as
addressing some short-comings therein. The new format will be
more self-describing than the HDF4 format and will be more
uniformly applied to data objects in the file.
<P>Three levels of information compose the file format. The level
0 contains basic information for identifying and
"boot-strapping" the file. Level 1 information is composed of
the object directory (stored as a B-tree) and is used as the
index for all the objects in the file. The rest of the file is
composed of data-objects at level 2, with each object
partitioned into header (or "meta") information and data
information.
<p>The sizes of various fields in the following layout tables are
determined by looking at the number of columns the field spans
in the table. There are three exceptions: (1) The size may be
overridden by specifying a size in parentheses, (2) the size of
addresses is determined by the <em>Size of Addresses</em> field
in the boot block, and (3) the size of size fields is determined
by the <em>Size of Sizes</em> field in the boot block.
<h3><a name="BootBlock">
Disk Format: Level 0 - File Signature and Boot Block</a></h3>
<P>The boot block may begin at certain predefined offsets within
the HDF5 file, allowing a block of unspecified content for
users to place additional information at the beginning (and
end) of the HDF5 file without limiting the HDF5 library's
ability to manage the objects within the file itself. This
feature was designed to accommodate wrapping an HDF5 file in
another file format or adding descriptive information to the
file without requiring the modification of the actual file's
information. The boot-block is located by searching for the
HDF5 file signature at byte offset 0, byte offset 512 and at
successive locations in the file, each a multiple of two of
the previous location, i.e. 0, 512, 1024, 2048, etc.
<P>The boot-block is composed of a file signature, followed by
boot block and object directory version numbers, information
about the sizes of offset and length values used to describe
items within the file, the size of each object directory page,
and a symbol table entry for the root object in the file.
<p>
<center>
<table border align=center cellpadding=4 width="80%">
<caption align=top>
<B>HDF5 Boot Block Layout</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4><br>HDF5 File Signature (8 bytes)<br><br></td>
</tr>
<tr align=center>
<td>Version # of Boot Block</td>
<td>Version # of Global Free-Space Storage</td>
<td>Version # of Object Directory</td>
<td>Reserved</td>
</tr>
<tr align=center>
<td>Version # of Shared Header Message Format</td>
<td>Size of Addresses</td>
<td>Size of Sizes</td>
<td>Reserved (zero)</td>
</tr>
<tr align=center>
<td colspan=2>Symbol Table Leaf Node K</td>
<td colspan=2>Symbol Table Internal Node K</td>
</tr>
<tr align=center>
<td colspan=4>File Consistency Flags</td>
</tr>
<tr align=center>
<td colspan=4>Base Address</td>
</tr>
<tr align=center>
<td colspan=4>Address of Global Free-Space Heap</td>
</tr>
<tr align=center>
<td colspan=4>End of File Address</td>
</tr>
<tr align=center>
<td colspan=4><br>
Symbol-Table Entry of the "Root Object"
<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>File Signature</td>
<td>This field contains a constant value and can be used to
quickly identify a file as being an HDF5 file. The
constant value is designed to allow easy identification of
an HDF5 file and to allow certain types of data corruption
to be detected. The file signature of a HDF5 file always
contain the following values:
<br><br><center>
<table border align=center cellpadding=4 width="80%">
<tr align=center>
<td>decimal</td>
<td width="8%">137</td>
<td width="8%">72</td>
<td width="8%">68</td>
<td width="8%">70</td>
<td width="8%">13</td>
<td width="8%">10</td>
<td width="8%">26</td>
<td width="8%">10</td>
</tr>
<tr align=center>
<td>hexadecimal</td>
<td width="8%">89</td>
<td width="8%">48</td>
<td width="8%">44</td>
<td width="8%">46</td>
<td width="8%">0d</td>
<td width="8%">0a</td>
<td width="8%">1a</td>
<td width="8%">0a</td>
</tr>
<tr align=center>
<td>ASCII C Notation</td>
<td width="8%">\211</td>
<td width="8%">H</td>
<td width="8%">D</td>
<td width="8%">F</td>
<td width="8%">\r</td>
<td width="8%">\n</td>
<td width="8%">\032</td>
<td width="8%">\n</td>
</tr>
</table>
</center>
<br>
This signature both identifies the file as a HDF5 file
and provides for immediate detection of common
file-transfer problems. The first two bytes distinguish
HDF5 files on systems that expect the first two bytes to
identify the file type uniquely. The first byte is
chosen as a non-ASCII value to reduce the probability
that a text file may be misrecognized as a HDF5 file;
also, it catches bad file transfers that clear bit
7. Bytes two through four name the format. The CR-LF
sequence catches bad file transfers that alter newline
sequences. The control-Z character stops file display
under MS-DOS. The final line feed checks for the inverse
of the CR-LF translation problem. (This is a direct
descendent of the PNG file signature.)</td>
</tr>
<tr valign=top>
<td>Version # of the Boot Block</td>
<td>This value is used to determine the format of the
information in the boot block. When the format of the
information in the boot block is changed, the version #
is incremented to the next integer and can be used to
determine how the information in the boot block is
formatted.</td>
</tr>
<tr valign=top>
<td>Version # of the Global Free-Space Storage</td>
<td>This value is used to determine the format of the
information in the Global Free-Space Heap. Currently,
this is implemented as a B-tree of length/offset pairs
to locate free space in the file, but future advances in
the file-format could change the method of finding
global free-space. When the format of the information
is changed, the version # is incremented to the next
integer and can be used to determine how the information
is formatted.</td>
</tr>
<tr valign=top>
<td>Version # of the Object Directory</td>
<td>This value is used to determine the format of the
information in the Object Directory. When the format of
the information in the Object Directory is changed, the
version # is incremented to the next integer and can be
used to determine how the information in the Object
Directory is formatted.</td>
</tr>
<tr valign=top>
<td>Version # of the Shared Header Message Format</td>
<td>This value is used to determine the format of the
information in a shared object header message, which is
stored in the global small-data heap. Since the format
of the shared header messages differ from the private
header messages, a version # is used to identify changes
in the format.</td>
</tr>
<tr valign=top>
<td>Size of Addresses</td>
<td>This value contains the number of bytes used for
addresses in the file. The values for the addresses of
objects in the file are relative to a base address,
usually the address of the boot block signature. This
allows a wrapper to be added after the file is created
without invalidating the internal offset locations.</td>
</tr>
<tr valign=top>
<td>Size of Sizes</td>
<td>This value contains the number of bytes used to store
the size of an object.</td>
</tr>
<tr valign=top>
<td>Symbol Table Leaf Node K</td>
<td>Each leaf node of a symbol table B-tree will have at
least this many entries but not more than twice this
many. If a symbol table has a single leaf node then it
may have fewer entries.</td>
</tr>
<tr valign=top>
<td>Symbol Table Internal Node K</td>
<td>Each internal node of a symbol table B-tree will have
at least K pointers to other nodes but not more than 2K
pointers. If the symbol table has only one internal
node then it might have fewer than K pointers.</td>
</tr>
<tr valign=top>
<td>Bytes per B-Tree Page</td>
<td>This value contains the # of bytes used for symbol
pairs per page of the B-Trees used in the file. All
B-Tree pages will have the same size per page. <br>(For
32-bit file offsets, 340 objects is the maximum per 4KB
page, and for 64-bit file offset, 254 objects will fit
per 4KB page. In general, the equation is: <br> <#
of objects> = FLOOR((<page size>-<offset
size>)/(<Symbol size>+<offset size>))-1 )</td>
</tr>
<tr valign=top>
<td>File Consistency Flags</td>
<td>This value contains flags to indicate information
about the consistency of the information contained
within the file. Currently, the following bit flags are
defined: bit 0 set indicates that the file is opened for
write-access and bit 1 set indicates that the file has
been verified for consistency and is guaranteed to be
consistent with the format defined in this document.
Bits 2-31 are reserved for future use. Bit 0 should be
set as the first action when a file is opened for write
access and should be cleared only as the final action
when closing a file. Bit 1 should be cleared during
normal access to a file and only set after the file's
consistency is guaranteed by the library or a
consistency utility.</td>
</tr>
<tr valign=top>
<td>Base Address</td>
<td>This is the absolute file address of the first byte of
the hdf5 data within the file. Unless otherwise noted,
all other file addresses are relative to this base
address.</td>
</tr>
<tr valign=top>
<td>Address of Global Free-Space Heap</td>
<td>This value contains the relative address of the B-Tree
used to manage the blocks of data which are unused in the
file currently. The free-space heap is used to manage the
blocks of bytes at the file-level which become unused with
objects are moved within the file.</td>
</tr>
<tr valign=top>
<td>End of File Address</td>
<td>This is the relative file address of the first byte past
the end of all HDF5 data. It is used to determine if a
file has been accidently truncated and as an address where
file memory allocation can occur if the free list is not
used.</td>
</tr>
<tr valign=top>
<td>Symbol-Table Entry of the Root Object</td>
<td>This symbol-table entry (described later in this
document) refers to the entry point into the group
graph. If the file contains a single object, then that
object can be the root object and no groups are used.</td>
</tr>
</table>
</center>
<h3><a name="Btrees">Disk Format: Level 1A - B-link Trees</a></h3>
<p>B-link trees allow flexible storage for objects which tend to grow
in ways that cause the object to be stored discontiguously. B-trees
are described in various algorithms books including "Introduction to
Algorithms" by Thomas H. Cormen, Charles E. Leiserson, and Ronald
L. Rivest. The B-link tree, in which the sibling nodes at a
particular level in the tree are stored in a doubly-linked list,
is described in the "Efficient Locking for Concurrent Operations
on B-trees" paper by Phillip Lehman and S. Bing Yao as published
in the <em>ACM Transactions on Database Systems</em>, Vol. 6,
No. 4, December 1981.
<p>The B-link trees implemented by the file format contain one more
key than the number of children. In other words, each child
pointer out of a B-tree node has a left key and a right key.
The pointers out of internal nodes point to sub-trees while
the pointers out of leaf nodes point to other file data types.
Notwithstanding that difference, internal nodes and leaf nodes
are identical.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>B-tree Nodes</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Node Signature</td>
<tr align=center>
<td>Node Type</td>
<td>Node Level</td>
<td colspan=2>Entries Used</td>
<tr align=center>
<td colspan=4>Address of Left Sibling</td>
<tr align=center>
<td colspan=4>Address of Right Sibling</td>
<tr align=center>
<td colspan=4>Key 0 (variable size)</td>
<tr align=center>
<td colspan=4>Address of Child 0</td>
<tr align=center>
<td colspan=4>Key 1 (variable size)</td>
<tr align=center>
<td colspan=4>Address of Child 1</td>
<tr align=center>
<td colspan=4>...</td>
<tr align=center>
<td colspan=4>Key 2<em>K</em> (variable size)</td>
<tr align=center>
<td colspan=4>Address of Child 2<em>K</em></td>
<tr align=center>
<td colspan=4>Key 2<em>K</em>+1 (variable size)</td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Node Signature</td>
<td>The value ASCII 'TREE' is used to indicate the
beginning of a B-link tree node. This gives file
consistency checking utilities a better chance of
reconstructing a damaged file.</td>
</tr>
<tr valign=top>
<td>Node Type</td>
<td>Each B-link tree points to a particular type of data.
This field indicates the type of data as well as
implying the maximum degree <em>K</em> of the tree and
the size of each Key field.
<br>
<dl compact>
<dt>0
<dd>This tree points to symbol table nodes.
<dt>1
<dd>This tree points to a (partial) linear address space.
</dl>
</td>
</tr>
<tr valign=top>
<td>Node Level</td>
<td>The node level indicates the level at which this node
appears in the tree (leaf nodes are at level zero). Not
only does the level indicate whether child pointers
point to sub-trees or to data, but it can also be used
to help file consistency checking utilities reconstruct
damanged trees.</td>
</tr>
<tr valign=top>
<td>Entries Used</td>
<td>This determines the number of children to which this
node points. All nodes of a particular type of tree
have the same maximum degree, but most nodes will point
to less than that number of children. The valid child
pointers and keys appear at the beginning of the node
and the unused pointers and keys appear at the end of
the node. The unused pointers and keys have undefined
values.</td>
</tr>
<tr valign=top>
<td>Address of Left Sibling</td>
<td>This is the file address of the left sibling of the
current node relative to the boot block. If the current
node is the left-most node at this level then this field
is the undefined address (all bits set).</td>
</tr>
<tr valign=top>
<td>Address of Right Sibling</td>
<td>This is the file address of the right sibling of the
current node relative to the boot block. If the current
node is the right-most node at this level then this
field is the undefined address (all bits set).</td>
</tr>
<tr valign=top>
<td>Keys and Child Pointers</td>
<td>Each tree has 2<em>K</em>+1 keys with 2<em>K</em>
child pointers interleaved between the keys. The number
of keys and child pointers actually containing valid
values is determined by the `Entries Used' field. If
that field is <em>N</em> then the B-link tree contains
<em>N</em> child pointers and <em>N</em>+1 keys.</td>
</tr>
<tr valign=top>
<td>Key</td>
<td>The format and size of the key values is determined by
the type of data to which this tree points. The keys are
ordered and are boundaries for the contents of the child
pointer. That is, the key values represented by child
<em>N</em> fall between Key <em>N</em> and Key
<em>N</em>+1. Whether the interval is open or closed on
each end is determined by the type of data to which the
tree points.</td>
</tr>
<tr valign=top>
<td>Address of Children</td>
<td>The tree node contains file addresses of subtrees or
data depending on the node level (0 implies data
addresses).</td>
</tr>
</table>
</center>
<h3><a name="SymbolTable">Disk Format: Level 1B - Symbol Table</a></h3>
<p>A symbol table is a group internal to the file that allows
arbitrary nesting of objects (including other symbol
tables). A symbol table maps a set of names to a set of file
address relative to the file boot block. Certain meta data
for an object to which the symbol table points can be cached
in the symbol table in addition to (or in place of?) the
object header.
<p>An HDF5 object name space can be stored hierarchically by
partitioning the name into components and storing each
component in a symbol table. The symbol table entry for a
non-ultimate component points to the symbol table containing
the next component. The symbol table entry for the last
component points to the object being named.
<p>A symbol table is a collection of symbol table nodes pointed
to by a B-link tree. Each symbol table node contains entries
for one or more symbols. If an attempt is made to add a
symbol to an already full symbol table node containing
2<em>K</em> entries, then the node is split and one node
contains <em>K</em> symbols and the other contains
<em>K</em>+1 symbols.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbol Table Node</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Node Signature</td>
<tr align=center>
<td>Version Number</td>
<td>Reserved for Future Use</td>
<td colspan=2>Number of Symbols</td>
<tr align=center>
<td colspan=4><br><br>Symbol Table Entries<br><br><br></td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Node Signature</td>
<td>The value ASCII 'SNOD' is used to indicate the
beginning of a symbol table node. This gives file
consistency checking utilities a better chance of
reconstructing a damaged file.</td>
</tr>
<tr valign=top>
<td>Version Number</td>
<td>The version number for the symbol table node. This
document describes version 1.</td>
</tr>
<tr valign=top>
<td>Number of Symbols</td>
<td>Although all symbol table nodes have the same length,
most contain fewer than the maximum possible number of
symbol entries. This field indicates how many entries
contain valid data. The valid entries are packed at the
beginning of the symbol table node while the remaining
entries contain undefined values.</td>
</tr>
<tr valign=top>
<td>Symbol Table Entries</td>
<td>Each symbol has an entry in the symbol table node.
The format of the entry is described below.</td>
</tr>
</table>
</center>
<h3><a name="SymbolTableEntry">
Disk Format: Level 1C - Symbol-Table Entry </a></h3>
<p>Each symbol table entry in a symbol table node is designed to allow
for very fast browsing of commonly stored scientific objects.
Toward that design goal, the format of the symbol-table entries
includes space for caching certain constant meta data from the
object header.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbol Table Entry</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Name Offset (<size> bytes)</td>
<tr align=center>
<td colspan=4>Object Header Address</td>
<tr align=center>
<td colspan=4>Symbol-Type</td>
<tr align=center>
<td colspan=4><br><br>Scratch-pad Space (24 bytes)<br><br><br></td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Name Offset</td>
<td>This is the byte offset into the symbol table local
heap for the name of the symbol. The name is null
terminated.</td>
</tr>
<tr valign=top>
<td>Object Header Address</td>
<td>Every object has an object header which serves as a
permanent home for the object's meta data. In addition
to appearing in the object header, the meta data can be
cached in the scratch-pad space.</td>
</tr>
<tr valign=top>
<td>Symbol-Type</td>
<td>The symbol type is determined from the object header.
It also determines the format for the scratch-pad space.
The value zero indicates that no object header meta data
is cached in the symbol table entry.
<br>
<dl compact>
<dt>0
<dd>No data is cached by the symbol table entry. This
is guaranteed to be the case when an object header
has a link count greater than one.
<dt>1
<dd>Symbol table meta data is cached in the symbol
table entry. This implies that the symbol table
entry refers to another symbol table.
<dt>2
<dd>The entry is a symbolic link. The first four bytes
of the scratch pad space are the offset into the local
heap for the link value. The object header address
will be undefined.
<dt><em>N</em>
<dd>Other cache values can be defined later and
libraries that don't understand the new values will
still work properly.
</dl>
</td>
</tr>
<tr valign=top>
<td>Scratch-Pad Space</td>
<td>This space is used for different purposes, depending
on the value of the Symbol Type field. Any meta-data
about a dataset object represented in the scratch-pad
space is duplicated in the object header for that
dataset. Furthermore, no data is cached in the symbol
table entry scratch-pad space if the object header for
the symbol table entry has a link count greater than
one.</td>
</tr>
</table>
</center>
<p>The symbol table entry scratch-pad space is formatted
according to the value of the Symbol Type field. If the
Symbol Type field has the value zero then no information is
stored in the scratch pad space.
<p>If the Symbol Type field is one, then the scratch pad space
contains cached meta data for another symbol table with the format:
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbol Table Scratch-Pad Format</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Address of B-tree</td>
<tr align=center>
<td colspan=4>Address of Name Heap</td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Address of B-tree</td>
<td>This is the file address for the symbol table's
B-tree.</td>
</tr>
<tr valign=top>
<td>Address of Name Heap</td>
<td>This is the file address for the symbol table's local
heap that stores the symbol names.</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Symbolic Link Scratch-Pad Format</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Offset to Link Value</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Offset to Link Value</td>
<td>The value of a symbolic link (that is, the name of the
thing to which it points) is stored in the local heap.
This field is the 4-byte offset into the local heap for
the start of the link value, which is null terminated.</td>
</tr>
</table>
</center>
<h3><a name="LocalHeap">Disk Format: Level 1D - Local Heaps</a></h3>
<p>A heap is a collection of small heap objects. Objects can be
inserted and removed from the heap at any time and the address
of a heap doesn't change once the heap is created. Note: this
is the "local" version of the heap mostly intended for the
storage of names in a symbol table. The storage of small
objects in a global heap is described below.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Local Heaps</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Heap Signature</td>
</tr>
<tr align=center>
<td colspan=4>Reserved (zero)</td>
</tr>
<tr align=center>
<td colspan=4>Data Segment Size</td>
</tr>
<tr align=center>
<td colspan=4>Offset to Head of Free-list (<size> bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Address of Data Segment</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Heap Signature</td>
<td>The valid ASCII 'HEAP' is used to indicate the
beginning of a heap. This gives file consistency
checking utilities a better chance of reconstructing a
damaged file.</td>
</tr>
<tr valign=top>
<td>Data Segment Size</td>
<td>The total amount of disk memory allocated for the heap
data. This may be larger than the amount of space
required by the object stored in the heap. The extra
unused space holds a linked list of free blocks.</td>
</tr>
<tr valign=top>
<td>Offset to Head of Free-list</td>
<td>This is the offset within the heap data segment of the
first free block (or all 0xff bytes if there is no free
block). The free block contains <size> bytes that
are the offset of the next free chunk (or all 0xff bytes
if this is the last free chunk) followed by <size>
bytes that store the size of this free chunk.</td>
</tr>
<tr valign=top>
<td>Address of Data Segment</td>
<td>The data segment originally starts immediately after
the heap header, but if the data segment must grow as a
result of adding more objects, then the data segment may
be relocated to another part of the file.</td>
</tr>
</table>
</center>
<p>Objects within the heap should be aligned on an 8-byte boundary.
<h3><a name="GlobalHeap">Disk Format: Level 1E - Global Heap</a></h3>
<p>Each HDF5 file has a global heap which stores various types of
information which is typically shared between datasets. The
global heap was designed to satisfy these goals:
<ol type="A">
<li>Repeated access to a heap object must be efficient without
resulting in repeated file I/O requests. Since global heap
objects will typically be shared among several datasets it's
probable that the object will be accessed repeatedly.
<br><br>
<li>Collections of related global heap objects should result in
fewer and larger I/O requests. For instance, a dataset of
void pointers will have a global heap object for each
pointer. Reading the entire set of void pointer objects
should result in a few large I/O requests instead of one small
I/O request for each object.
<br><br>
<li>It should be possible to remove objects from the global heap
and the resulting file hole should be eligible to be reclaimed
for other uses.
<br><br>
</ol>
<p>The implementation of the heap makes use of the memory
management already available at the file level and combines that
with a new top-level object called a <em>collection</em> to
achieve Goal B. The global heap is the set of all collections.
Each global heap object belongs to exactly one collection and
each collection contains one or more global heap objects. For
the purposes of disk I/O and caching, a collection is treated as
an atomic object.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Global Heap Collection</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4>Magic Number</td>
</tr>
<tr align=center>
<td>Version</td>
<td colspan=3>Reserved</td>
</td>
<tr align=center>
<td colspan=4>Collection Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Object 1<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Object 2<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>...<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Object <em>N</em><br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Object 0 (free space)<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Magic Number</td>
<td>The magic number for global heap collections are the
four bytes `G', `C', `O', `L'.</td>
</tr>
<tr valign=top>
<td>Version</td>
<td>Each collection has its own version number so that new
collections can be added to old files. This document
describes version zero of the collections.
</tr>
<tr valign=top>
<td>Collection Data Size</td>
<td>This is the size in bytes of the entire collection
including this field. The default (and minimum)
collection size is 4096 bytes which is a typical file
system block size and which allows for 170 16-byte heap
objects plus their overhead.</td>
</tr>
<tr valign=top>
<td>Object <em>i</em> for positive <em>i</em></td> <td>The
objects are stored in any order with no intervening unused
space.</td>
</tr>
<tr valign=top>
<td>Object 0</td>
<td>Object zero, when present, represents the free space in
the collection. Free space always appears at the end of
the collection. If the free space is too small to store
the header for object zero (described below) then the
header is implied.
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Global Heap Object</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=2>Object ID</td>
<td colspan=2>Reference Count</td>
</tr>
<tr align=center>
<td colspan=4>Object Total Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Object Data<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Object ID</td>
<td>Each object has a unique identification number within a
collection. The identification numbers are chosen so that
new objects have the smallest value possible with the
exception that the identifier `0' always refers to the
object which represents all free space within the
collection.</td>
</tr>
<tr valign=top>
<td>Reference Count</td>
<td>All heap objects have a reference count field. An
object which is referenced from some other part of the
file will have a positive reference count. The reference
count for Object zero is always zero.</td>
</tr>
<tr valign=top>
<td>Object Total Size</td>
<td>This is the total size in bytes of the object. It
includes all fields listed in this table.</td>
</tr>
<tr valign=top>
<td>Object Data</td>
<td>The object data is treated as a one-dimensional array
of bytes to be interpreted by the caller.</td>
</tr>
</table>
</center>
<h3><a name="FreeSpaceIndex">Disk Format: Level 1F - Free-Space
Index (NOT FULLY DEFINED)</a></h3>
<p>The Free-Space Index is a collection of blocks of data,
dispersed throughout the file, which are currently not used by
any file objects. The blocks of data are indexed by a B-tree of
their length within the file.
<p>Each B-Tree page is composed of the following entries and
B-tree management information, organized as follows:
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Free-Space Heap Page</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Free-Space Heap Signature</td>
<tr align=center>
<td colspan=4>B-Tree Left-Link Offset</td>
<tr align=center>
<td colspan=4><br>Length of Free-Block #1<br> <br></td>
<tr align=center>
<td colspan=4><br>Offset of Free-Block #1<br> <br></td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4><br>Length of Free-Block #n<br> <br></td>
<tr align=center>
<td colspan=4><br>Offset of Free-Block #n<br> <br></td>
<tr align=center>
<td colspan=4>"High" Offset</td>
<tr align=center>
<td colspan=4>Right-Link Offset</td>
</table>
</center>
<p>
<dl>
<dt> The elements of the free-space heap page are described below:
<dd>
<dl>
<dt>Free-Space Heap Signature: (4 bytes)
<dd>The value ASCII: 'FREE' is used to indicate the
beginning of a free-space heap B-Tree page. This gives
file consistency checking utilities a better chance of
reconstructing a damaged file.
<dt>B-Tree Left-Link Offset: (<offset> bytes)
<dd>This value is used to indicate the offset of all offsets
in the B-link-tree which are smaller than the value of the
offset in entry #1. This value is also used to indicate a
leaf node in the B-link-tree by being set to all ones.
<dt>Length of Free-Block #n: (<length> bytes)
<dd>This value indicates the length of an un-used block in
the file.
<dt>Offset of Free-Block #n: (<offset> bytes)
<dd>This value indicates the offset in the file of an
un-used block in the file.
<dt>"High" Offset: (4-bytes)
<dd>This offset is used as the upper bound on offsets
contained within a page when the page has been split.
<dt>Right-link Offset: (<offset> bytes)
<dd>This value is used to indicate the offset of the next
child to the right of the parent of this object directory
page. When there is no node to the right, this value is
all zeros.
</dl>
</dl>
<p>The algorithms for searching and inserting objects in the
B-tree pages are described fully in the Lehman & Yao paper,
which should be read to provide a full description of the
B-Tree's usage.
<h3><a name="DataObject">Disk Format: Level 2 - Data Objects </a></h3>
<p>Data objects contain the real information in the file. These
objects compose the scientific data and other information which
are generally thought of as "data" by the end-user. All the
other information in the file is provided as a framework for
these data objects.
<p>A data object is composed of header information and data
information. The header information contains the information
needed to interpret the data information for the data object as
well as additional "meta-data" or pointers to additional
"meta-data" used to describe or annotate each data object.
<h3><a name="ObjectHeader">
Disk Format: Level 2a - Data Object Headers</a></h3>
<p>The header information of an object is designed to encompass
all the information about an object which would be desired to be
known, except for the data itself. This information includes
the dimensionality, number-type, information about how the data
is stored on disk (in external files, compressed, broken up in
blocks, etc.), as well as other information used by the library
to speed up access to the data objects or maintain a file's
integrity. The header of each object is not necessarily located
immediately prior to the object's data in the file and in fact
may be located in any position in the file.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Object Headers</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=1 width="25%">Version # of Object Header</td>
<td colspan=1 width="25%">Alignment of Object Header Messages</td>
<td colspan=2 width="50%">Number of Header Messages</td>
</tr>
<tr align=center>
<td colspan=4>Object Reference Count</td>
</tr>
<tr align=center>
<td colspan=4><br>Total Object-Header Size<br><br></td>
</tr>
<tr align=center>
<td colspan=2>Header Message Type #1</td>
<td colspan=2>Size of Header Message Data #1</td>
</tr>
<tr align=center>
<td>Flags</td>
<td colspan=3>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Header Message Data #1 (variable size)</td>
</tr>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr align=center>
<td colspan=2>Header Message Type #n</td>
<td colspan=2>Size of Header Message Data #n</td>
</tr>
<tr align=center>
<td>Flags</td>
<td colspan=3>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Header Message Data #n (variable)</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Version # of the object header</td>
<td>This value is used to determine the format of the
information in the object header. When the format of the
information in the object header is changed, the version #
is incremented and can be used to determine how the
information in the object header is formatted.</td>
</tr>
<tr valign=top>
<td>Alignment of object header messages</td>
<td>This value is used to determine the byte-alignment of
messagesin the object header. Typically set to 4, which
aligns new messages on a 4-byte boundary in the object
header.</td>
</tr>
<tr valign=top>
<td>Number of header messages</td>
<td>This value determines the number of messages listed in
this object header. This provides a fast way for software
to prepare storage for the messages in the header.</td>
</tr>
<tr valign=top>
<td>Object Reference Count</td>
<td>This value specifies the number of references to this
object within the current file. References to the
data-object from external files are not tracked.</td>
</tr>
<tr valign=top>
<td>Total Object-Header Size</td>
<td>This value specifies the total number of bytes of header
message data following this length field for the current
message as well as any continuation data located elsewhere
in the file.</td>
</tr>
<tr valign=top>
<td>Header Message Type</td>
<td>The header message type specifies the type of
information included in the header message data following
the type along with a small amount of other information.
Bit 15 of the message type is set if the message is
constant (constant messages cannot be changed since they
may be cached in symbol table entries throughout the
file). The header message types for the pre-defined
header messages will be included in further discussion
below.</td>
</tr>
<tr valign=top>
<td>Size of Header Message Data</td>
<td>This value specifies the number of bytes of header
message data following the header message type and length
information for the current message.</td>
</tr>
<tr valign=top>
<td>Flags</td>
<td>This is a bit field with the following definition:
<dl>
<dt><code>0</code>
<dd>If set, the message data is constant. This is used
for messages like the data type message of a dataset.
<dt><code>1</code>
<dd>If set, the message is stored in the global heap and
the Header Message Data field contains a Shared Object
message. and the Size of Header Message Data field
contains the size of that Shared Object message.
<dt><code>2-7</code>
<dd>Reserved
</dl>
</td>
<tr valign=top>
<td>Header Message Data</td>
<td>The format and length of this field is determined by the
header message type and size respectively. Some header
message types do not require any data and this information
can be eliminated by setting the length of the message to
zero.</td>
</tr>
</table>
</center>
<p>The header message types and the message data associated with
them compose the critical "meta-data" about each object. Some
header messages are required for each object while others are
optional. Some optional header messages may also be repeated
several times in the header itself, the requirements and number
of times allowed in the header will be noted in each header
message description below.
<P>The following is a list of currently defined header messages:
<hr>
<h3><a name="NILMessage">Name: NIL</a></h3>
<b>Type: </b>0x0000<br>
<b>Length:</b> varies<br>
<b>Status:</b> Optional, may be repeated.<br>
<b>Purpose and Description:</b> The NIL message is used to
indicate a message
which is to be ignored when reading the header messages for a data object.
[Probably one which has been deleted for some reason.]<br>
<b>Format of Data:</b> Unspecified.<br>
<b>Examples:</b> None.
<hr>
<h3><a name="SimpleDataSpace">Name: Simple Data Space/a></h3>
<b>Type: </b>0x0001<br>
<b>Length:</b> varies<br>
<b>Status:</b> One of the <em>Simple Data Space</em> or
<em>Data-Space</em> messages is required (but not both) and may
not be repeated.<br>
<p>The <em>Simple Dimensionality</em> message describes the number
of dimensions and size of each dimension that the data object
has. This message is only used for datasets which have a
simple, rectilinear grid layout, datasets requiring a more
complex layout (irregularly or unstructured grids, etc) must use
the <em>Data-Space</em> message for expressing the space the
dataset inhabits.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Simple Data Space Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Dimensionality</td>
<tr align=center>
<td colspan=4>Dimension Flags</td>
<tr align=center>
<td colspan=4>Dimension Size #1 (<size> bytes)</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Dimension Size #n (<size> bytes)</td>
<tr align=center>
<td colspan=4>Dimension Maximum #1 (<size> bytes)</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Dimension Maximum #n (<size> bytes)</td>
<tr align=center>
<td colspan=4>Permutation Index #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Permutation Index #n</td>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Dimensionality</td>
<td>This value is the number of dimensions that the data
object has.</td>
</tr>
<tr valign=top>
<td>Dimension Flags</td>
<td>This field is used to store flags to indicate the
presence of parts of this message. Bit 0 (counting from
the right) is used to indicate that maximum dimensions are
present. Bit 1 is used to indicate that permutation
indices are present for each dimension.</td>
</tr>
<tr valign=top>
<td>Dimension Size #n (<size&rt; bytes)</td>
<td>This value is the current size of the dimension of the
data as stored in the file. The first dimension stored in
the list of dimensions is the slowest changing dimension
and the last dimension stored is the fastest changing
dimension.</td>
</tr>
<tr valign=top>
<td>Dimension Maximum #n (<size&rt; bytes)</td>
<td>This value is the maximum size of the dimension of the
data as stored in the file. This value may be the special
value <UNLIMITED> (0xffffffff) which indicates that
the data may expand along this dimension indefinitely. If
these values are not stored, the maximum value of each
dimension is assumed to be the same as the current size
value.</td>
</tr>
<tr valign=top>
<td>Permutation Index #n (4 bytes)</td>
<td>This value is the index permutation used to map
each dimension from the canonical representation to an
alternate axis for each dimension. If these values are
not stored, the first dimension stored in the list of
dimensions is the slowest changing dimension and the last
dimension stored is the fastest changing dimension.</td>
</tr>
</table>
</center>
<h4>Examples</h4>
<dl>
<dt> Example #1
<dd>A sample 640 horizontally by 480 vertically raster image
dimension header. The number of dimensions would be set to 2
and the first dimension's size and maximum would both be set
to 480. The second dimension's size and maximum would both be
set to 640
.
<dt>Example #2
<dd>A sample 4 dimensional scientific dataset which is composed
of 30x24x3 slabs of data being written out in an unlimited
series every several minutes as timestep data (currently there
are five slabs). The number of dimensions is 4. The first
dimension size is 5 and it's maximum is <UNLIMITED>. The
second through fourth dimensions' size and maximum value are
set to 3, 24, and 30 respectively.
<dt>Example #3
<dd>A sample unlimited length text string, currently of length
83. The number of dimensions is 1, the size of the first
dimension is 83 and the maximum of the first dimension is set
to <UNLIMITED>, allowing further text data to be
appended to the string or possibly the string to be replaced
with another string of a different size. (This could also be
stored as a scalar dataset with number-type set to "string")
</dl>
<hr>
<h3><a name="DataSpaceMessage">Name: Data-Space (Fiber Bundle?)</a></h3>
<b>Type: </b>0x0002<br>
<b>Length:</b> varies<br>
<b>Status:</b> One of the <em>Simple Dimensionality</em> or
<em>Data-Space</em> messages is required (but not both) and may
not be repeated.<br> <b>Purpose and Description:</b> The
<em>Data-Space</em> message describes space that the dataset is
mapped onto in a more comprehensive way than the <em>Simple
Dimensionality</em> message is capable of handling. The
data-space of a dataset encompasses the type of coordinate system
used to locate the dataset's elements as well as the structure and
regularity of the coordinate system. The data-space also
describes the number of dimensions which the dataset inhabits as
well as a possible higher dimensional space in which the dataset
is located within.
<br>
<b>Format of Data:</b>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Message Layout</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Mesh Type</td>
<tr align=center>
<td colspan=4>Logical Dimensionality</td>
</table>
</center>
<p>
<dl>
<dt>The elements of the dimensionality message are described below:
<dd>
<dl>
<dt>Mesh Type: (unsigned 32-bit integer)
<dd>This value indicates whether the grid is
polar/spherical/cartesion,
structured/unstructured and regular/irregular. <br>
The mesh type value is broken up as follows: <br>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Mesh-Type Layout</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=1>Mesh Embedding</td>
<td colspan=1>Coordinate System</td>
<td colspan=1>Structure</td>
<td colspan=1>Regularity</td>
</table>
</center>
The following are the definitions of mesh-type bytes:
<dl>
<dt>Mesh Embedding
<dd>This value indicates whether the dataset data-space
is located within
another dataspace or not:
<dl> <dl>
<dt><STANDALONE>
<dd>The dataset mesh is self-contained and is not
embedded in another mesh.
<dt><EMBEDDED>
<dd>The dataset's data-space is located within
another data-space, as
described in information below.
</dl> </dl>
<dt>Coordinate System
<dd>This value defines the type of coordinate system
used for the mesh:
<dl> <dl>
<dt><POLAR>
<dd>The last two dimensions are in polar
coordinates, higher dimensions are
cartesian.
<dt><SPHERICAL>
<dd>The last three dimensions are in spherical
coordinates, higher dimensions
are cartesian.
<dt><CARTESIAN>
<dd>All dimensions are in cartesian coordinates.
</dl> </dl>
<dt>Structure
<dd>This value defines the locations of the grid-points
on the axes:
<dl> <dl>
<dt><STRUCTURED>
<dd>All grid-points are on integral, sequential
locations, starting from 0.
<dt><UNSTRUCTURED>
<dd>Grid-points locations in each dimension are
explicitly defined and
may be of any numeric data-type.
</dl> </dl>
<dt>Regularity
<dd>This value defines the locations of the dataset
points on the grid:
<dl> <dl>
<dt><REGULAR>
<dd>All dataset elements are located at the
grid-points defined.
<dt><IRREGULAR>
<dd>Each dataset element has a particular
grid-location defined.
</dl> </dl>
</dl>
<p>The following grid combinations are currently allowed:
<dl> <dl>
<dt><POLAR-STRUCTURED-REGULAR>
<dt><SPHERICAL-STRUCTURED-REGULAR>
<dt><CARTESIAN-STRUCTURED-REGULAR>
<dt><POLAR-UNSTRUCTURED-REGULAR>
<dt><SPHERICAL-UNSTRUCTURED-REGULAR>
<dt><CARTESIAN-UNSTRUCTURED-REGULAR>
<dt><CARTESIAN-UNSTRUCTURED-IRREGULAR>
</dl> </dl>
All of the above grid types can be embedded within another
data-space.
<br> <br>
<dt>Logical Dimensionality: (unsigned 32-bit integer)
<dd>This value is the number of dimensions that the dataset occupies.
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Embedded Dimensionality Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Embedded Dimensionality</td>
<tr align=center>
<td colspan=4>Embedded Dimension Size #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Embedded Dimension Size #n</td>
<tr align=center>
<td colspan=4>Embedded Origin Location #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Embedded Origin Location #n</td>
</table>
</center>
<dt>Embedded Dimensionality: (unsigned 32-bit integer)
<dd>This value is the number of dimensions of the space the
dataset is located
within. i.e. a planar dataset located within a 3-D space,
or a 3-D dataset
which is a subset of another 3-D space, etc.
<dt>Embedded Dimension Size: (unsigned 32-bit integer)
<dd>These values are the sizes of the dimensions of the
embedded data-space
that the dataset is located within.
<dt>Embedded Origin Location: (unsigned 32-bit integer)
<dd>These values comprise the location of the dataset's
origin within the embedded data-space.
</dl>
</dl>
[Comment: need some way to handle different orientations of the
dataset data-space
within the embedded data-space]<br>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Structured/Regular Grid Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Logical Dimension Size #1</td>
<tr align=center>
<td colspan=4>Logical Dimension Maximum #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Logical Dimension Size #n</td>
<tr align=center>
<td colspan=4>Logical Dimension Maximum #n</td>
</table>
</center>
<p>
<dl>
<dt>The elements of the dimensionality message are described below:
<dd>
<dl>
<dt>Logical Dimension Size #n: (unsigned 32-bit integer)
<dd>This value is the current size of the dimension of the
data as stored in
the file. The first dimension stored in the list of
dimensions is the slowest
changing dimension and the last dimension stored is the
fastest changing
dimension.
<dt>Logical Dimension Maximum #n: (unsigned 32-bit integer)
<dd>This value is the maximum size of the dimension of the
data as stored in
the file. This value may be the special value
<UNLIMITED> which
indicates that the data may expand along this dimension
indefinitely.
</dl>
</dl>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Structured/Irregular Grid Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4># of Grid Points in Dimension #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4># of Grid Points in Dimension #n</td>
<tr align=center>
<td colspan=4>Data-Type of Grid Point Locations</td>
<tr align=center>
<td colspan=4>Location of Grid Points in Dimension #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Location of Grid Points in Dimension #n</td>
</table>
</center>
<P>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<B>HDF5 Data-Space Unstructured Grid Information</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4># of Grid Points</td>
<tr align=center>
<td colspan=4>Data-Type of Grid Point Locations</td>
<tr align=center>
<td colspan=4>Grid Point Locations<br>.<br>.<br></td>
</table>
</center>
<h4><a name="DataSpaceExample">Examples:</a></h4>
Need some good examples, this is complex!
<hr>
<h3><a name="DataTypeMessage">Name: Data Type</a></h3>
<b>Type:</b> 0x0003<br>
<b>Length:</b> variable<br>
<b>Status:</b> One required per dataset<br>
<p>The data type message defines the data type for each data point
of a dataset. A data type can describe an atomic type like a
fixed- or floating-point type or a compound type like a C
struct. A data type does not, however, describe how data points
are combined to produce a dataset. Data types are stored on disk
as a data type message, which is a list of data type classes and
their associated properties.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Data Type Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Type Class</td>
<td colspan=3>Class Bit Field</td>
</tr>
<tr align=center>
<td colspan=4>Size in Bytes (4 bytes)</td>
</tr>
<tr align=center>
<td colspan=4><br><br>Properties<br><br><br></td>
</tr>
</table>
</center>
<p>The Class Bit Field and Properties fields vary depending
on the Type Class. The type class is one of: 0 (fixed-point
number), 1 (floating-point number), 2 (date and time), 3 (text
string), 4 (bit field), 5 (opaque), 6 (compound). The Class Bit
Field is zero and the size of the Properties field is zero
except for the cases noted here.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Bit Field for Fixed-Point Numbers (Class 0)</b>
</caption>
<tr align=center>
<th width="10%">Bits</th>
<th width="90%">Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<td>1, 2</td>
<td><b>Padding type.</b> Bit 1 is the lo_pad type and bit 2
is the hi_pad type. If a datum has unused bits at either
end, then the lo_pad or hi_pad bit is copied to those
locations.</td>
</tr>
<tr>
<td>3</td>
<td><b>Signed.</b> If this bit is set then the fixed-point
number is in 2's complement form.</td>
</tr>
<tr>
<td>4-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Properties for Fixed-Point Numbers (Class 0)</b>
</caption>
<tr align=center>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr align=center>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Bit Field for Floating-Point Numbers (Class 1)</b>
</caption>
<tr align=center>
<th width="10%">Bits</th>
<th width="90%">Meaning</th>
</tr>
<tr>
<td>0</td>
<td><b>Byte Order.</b> If zero, byte order is little-endian;
otherwise, byte order is big endian.</td>
</tr>
<tr>
<td>1, 2, 3</td>
<td><b>Padding type.</b> Bit 1 is the low bits pad type, bit 2
is the high bits pad type, and bit 3 is the internal bits
pad type. If a datum has unused bits at either or between
the sign bit, exponent, or mantissa, then the value of bit
1, 2, or 3 is copied to those locations.</td>
</tr>
<tr>
<td>4-5</td>
<td><b>Normalization.</b> The value can be 0 if there is no
normalization, 1 if the most significant bit of the
mantissa is always set (except for 0.0), and 2 if the most
signficant bit of the mantissa is not stored but is
implied to be set. The value 3 is reserved and will not
appear in this field.</td>
</tr>
<tr>
<td>6-7</td>
<td>Reserved (zero).</td>
</tr>
<tr>
<td>8-15</td>
<td><b>Sign.</b> This is the bit position of the sign
bit.</td>
</tr>
<tr>
<td>16-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Properties for Floating-Point Numbers (Class 1)</b>
</caption>
<tr align=center>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr align=center>
<td colspan=2>Bit Offset</td>
<td colspan=2>Bit Precision</td>
</tr>
<tr align=center>
<td>Exponent Location</td>
<td>Exponent Size in Bits</td>
<td>Mantissa Location</td>
<td>Mantissa Size in Bits</td>
</tr>
<tr align=center>
<td colspan=4>Exponent Bias</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<b>Bit Field for Compound Types (Class 6)</b>
</caption>
<tr align=center>
<th width="10%">Bits</th>
<th width="90%">Meaning</th>
</tr>
<tr>
<td>0-15</td>
<td><b>Number of Members.</b> This field contains the number
of members defined for the compound data type. The member
definitions are listed in the Properties field of the data
type message.
</tr>
<tr>
<td>15-23</td>
<td>Reserved (zero).</td>
</tr>
</table>
</center>
<p>The Properties field of a compound data type is a list of the
member definitions of the compound data type. The member
definitions appear one after another with no intervening bytes.
The member types are described with a recursive data type
message.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<b>Properties for Compound Types (Class 6)</b>
</caption>
<tr align=center>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
<th width="25%">Byte</th>
</tr>
<tr align=center>
<td colspan=4><br><br>Name (null terminated, multiple of
four bytes)<br><br><br></td>
</tr>
<tr align=center>
<td colspan=4>Byte Offset of Member in Compound Instance</td>
</tr>
<tr>
<td>Dimensionality</td>
<td colspan=3>reserved</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 0 (optional)</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 1 (optional)</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 2 (optional)</td>
</tr>
<tr align=center>
<td colspan=4>Size of Dimension 3 (optional)</td>
</tr>
<tr align=center>
<td colspan=4>Dimension Permutation</td>
</tr>
<tr align=center>
<td colspan=4><br><br>Member Type Message<br><br><br></td>
</tr>
</table>
</center>
<p>Data type examples are <a href="Datatypes.html">here</a>.
<hr>
<h3><a name="ReservedMessage_0004">Name: Reserved - Not Assigned
Yet</a></h3>
<b>Type:</b> 0x0004<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<hr>
<h3><a name="ReservedMessage_0005">Name: Reserved - Not Assigned
Yet</a></h3>
<b>Type:</b> 0x0005<br>
<b>Length:</b> N/A<br>
<b>Status:</b> N/A<br>
<hr>
<h3><a name="CompactDataStorageMessage">Name: Data Storage - Compact</a></h3>
<b>Type:</b> 0x0006<br>
<b>Length:</b> varies<br>
<b>Status:</b> Optional, may not be repeated.<br>
<p>This message indicates that the data for the data object is
stored within the current HDF file by including the actual
data within the header data for this message. The data is
stored internally in
the "normal" format, i.e. in one chunk, un-compressed, etc.
<P>Note that one and only one of the "Data Storage" headers can be
stored for each data object.
<P><b>Format of Data:</b> The message data is actually composed
of dataset data, so the format will be determined by the dataset
format.
<h4><a name="CompactDataStorageExample">Examples:</a></h4>
[very straightforward]
<hr>
<h3><a name="ExternalFileListMessage">Name: Data Storage -
External Data Files</a></h3>
<b>Type:</b> 0x0007<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may not be repeated.<BR>
<p><b>Purpose and Description:</b> The external object message
indicates that the data for an object is stored outside the HDF5
file. The filename of the object is stored as a Universal
Resource Location (URL) of the actual filename containing the
data. An external file list record also contains the byte offset
of the start of the data within the file and the amount of space
reserved in the file for that data.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>External File List Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4><br>Heap Address<br><br></td>
</tr>
<tr align=center>
<td colspan=2>Allocated Slots</td>
<td colspan=2>Used Slots</td>
</tr>
<tr align=center>
<td colspan=4>Reserved</td>
</tr>
<tr align=center>
<td colspan=4><br>Slot Definitions...<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Heap Address</td>
<td>This is the address of a local name heap which contains
the names for the external files. The name at offset zero
in the heap is always the empty string.</td>
</tr>
<tr valign=top>
<td>Allocated Slots</td>
<td>The total number of slots allocated in the message. Its
value must be at least as large as the value contained in
the Used Slots field.</td>
</tr>
<tr valign=top>
<td>Used Slots</td>
<td>The number of initial slots which contain valid
information. The remaining slots are zero filled.</td>
</tr>
<tr valign=top>
<td>Reserved</td>
<td>This field is reserved for future use.</td>
</tr>
<tr valign=top>
<td>Slot Definitions</td>
<td>The slot definitions are stored in order according to
the array addresses they represent. If more slots have
been allocated than what has been used then the defined
slots are all at the beginning of the list.</td>
</tr>
</table>
</center>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>External File List Slot</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4><br>Name Offset (<size> bytes)<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>File Offset (<size> bytes)<br><br></td>
</tr>
<tr align=center>
<td colspan=4><br>Size<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Name Offset (<size> bytes)</td>
<td>The byte offset within the local name heap for the name
of the file. File names are stored as a URL which has a
protocol name, a host name, a port number, and a file
name:
<code><em>protocol</em>:<em>port</em>//<em>host</em>/<em>file</em></code>.
If the protocol is omitted then "file:" is assumed. If
the port number is omitted then a default port for that
protocol is used. If both the protocol and the port
number are omitted then the colon can also be omitted. If
the double slash and host name are omitted then
"localhost" is assumed. The file name is the only
mandatory part, and if the leading slash is missing then
it is relative to the application's current working
directory (the use of relative names is not
recommended).</td>
</tr>
<tr valign=top>
<td>File Offset (<size> bytes)</td>
<td>This is the byte offset to the start of the data in the
specified file. For files that contain data for a single
dataset this will usually be zero.</td>
</tr>
<tr valign=top>
<td>Size</td>
<td>This is the total number of bytes reserved in the
specified file for raw data storage. For a file that
contains exactly one complete dataset which is not
extendable, the size will usually be the exact size of the
dataset. However, by making the size larger one allows
HDF5 to extend the dataset. The size can be set to a value
larger than the entire file since HDF5 will read zeros
past the end of the file without failing.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="LayoutMessage">Name: Data Storage - Layout</a></h3>
<b>Type:</b> 0x0008<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Required for datasets, may not be repeated.
<p><b>Purpose and Description:</b> Data layout describes how the
elements of a multi-dimensional array are arranged in the linear
address space of the file. Two types of data layout are
supported:
<ol>
<li>The array can be stored in one contiguous area of the file.
The layout requires that the size of the array be constant and
does not permit chunking or compression. The message stores
the total size of the array and the offset of an element from
the beginning of the storage area is computed as in C.
<li>The array domain can be regularly decomposed into chunks and
each chunk is allocated separately. This layout supports
arbitrary element traversals and compression and the chunks
can be distributed across external raw data files (these
features are described in other messages). The message stores
the size of a chunk instead of the size of the entire array;
the size of the entire array can be calculated by traversing
the B-tree that stores the chunk addresses.
</ol>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<B>Data Layout Message</B>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td colspan=4><br>Address<br><br></td>
</tr>
<tr align=center>
<td>Dimensionality</td>
<td>Layout Class</td>
<td colspan=2>Reserved</td>
</tr>
<tr align=center>
<td colspan=4>Reserved (4-bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Dimension 0 (4-bytes)</td>
</tr>
<tr align=center>
<td colspan=4>Dimension 1 (4-bytes)</td>
</tr>
<tr align=center>
<td colspan=4>...</td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Address</td>
<td>For contiguous storage, this is the address of the first
byte of storage. For chunked storage this is the address
of the B-tree that is used to look up the addresses of the
chunks.</td>
</tr>
<tr valign=top>
<td>Dimensionality</td>
<td>An array has a fixed dimensionality. This field
specifies the number of dimension size fields later in the
message.</td>
</tr>
<tr valign=top>
<td>Layout Class</td>
<td>The layout class specifies how the other fields of the
layout message are to be interpreted. A value of one
indicates contiguous storage while a value of two
indicates chunked storage. Other values will be defined
in the future.</td>
</tr>
<tr valign=top>
<td>Dimensions</td>
<td>For contiguous storage the dimensions define the entire
size of the array while for chunked storage they define
the size of a single chunk.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="ReservedMessage_0009">Name: Reserved - Not Assigned Yet</a></h3>
<b>Type:</b> 0x0009<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Purpose and Description:</b> N/A<BR>
<b>Format of Data:</b> N/A
<hr>
<h3><a name="ReservedMessage_000A">Name: Reserved - Not Assigned Yet</a></h3>
<b>Type:</b> 0x000A<BR>
<b>Length:</b> N/A<BR>
<b>Status:</b> N/A<BR>
<b>Purpose and Description:</b> N/A<BR>
<b>Format of Data:</b> N/A
<hr>
<h3><a name="CompressionMessage">Name: Data Storage - Compressed</a></h3>
<b>Type:</b> 0x000B<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may not be repeated.
<p><b>Purpose and Description:</b> Compressed objects are
datasets which are stored in an HDF file after they have been
compressed. The encoding algorithm and its parameters are
stored in a Compression Message in the object header of the
dataset.
<p>
<center>
<table border align=center cellpadding=4 witdh="80%">
<caption align=top>
<b>Compression Message</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
</tr>
<tr align=center>
<td>Method</td>
<td>Flags</td>
<td colspan=2>Client Data Size</td>
</tr>
<tr align=center>
<td colspan=4><br>Client Data<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Method</td>
<td>The compression method is a value between zero and 255,
inclusive, that is used as a index into a compression
method lookup table. The value zero indicates no
compression. The values one through 15, inclusive, are
reserved for methods defined by NCSA. All other values
are user-defined compression methods.</td>
</tr>
<tr valign=top>
<td>Flags</td>
<td>Eight bits of flags which are passed to the compression
algorithm. There meaning depends on the compression
method.</td>
</tr>
<tr valign=top>
<td>Client Data Size</td>
<td>The size in bytes of the optional Client Data
field.</td>
</tr>
<tr valign=top>
<td>Client Data</td>
<td>Additional information needed by the compression method
can be stored in this field. The data will be passed to
the compression algorithm as a void pointer.</td>
</tr>
</table>
</center>
<p>Sometimes additional redundancy can be added to the data before
it's compressed to result in a better compression ratio. The
library doesn't specifically support modeling methods to add
redundancy, but the effect can be achieved through the use of
user-defined data types.
<p>The library uses the following compression methods.
<center>
<table align=center width="80%">
<tr valign=top>
<td><code>0</code></td>
<td>No compression: The blocks of data are stored in
their raw format.</td>
</tr>
<tr valign=top>
<td><code>1</code></td>
<td>Deflation: This is the same algorithm used by
GNU gzip which is a combination Huffman and LZ77
dictionary encoder. The <code>libz</code> library version
1.1.2 or later must be available.</td>
</tr>
<tr valign=top>
<td><code>2</code></td>
<td>Run length encoding: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>3</code></td>
<td>Adaptive Huffman: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>4</code></td>
<td>Adaptive Arithmetic: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>5</code></td>
<td>LZ78 Dictionary Encoding: Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>6</code></td>
<td>Adaptive Lempel-Ziv: Similar to Unix
<code>compress</code>. Not implemented yet.</td>
</tr>
<tr valign=top>
<td><code>7-15</code></td>
<td>Reserved for future use.</td>
</tr>
<tr valign=top>
<td><code>16-255</code></td>
<td>User-defined.</td>
</tr>
</table>
</center>
<p>The compression is applied independently to each chunk of
storage (after data space and data type conversions). If the
compression is unable to make the chunk smaller than it would
normally be, the chunk is stored without compression. At the
library's discretion, chunks which fail the compression can also
be stored in their raw format.
<!--
<hr>
<h3><a name="BackPointerMessage">Name: Back-Pointer List</a></h3>
<b>Type:</b> 0x000C<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may be repeated.<BR>
<b>Purpose and Description:</b> The back-pointer message contains a list of
other objects which reference the current object and a reference count of the
number the current object is referenced. External references (i.e. references
to objects in the current HDF file from outside HDF files) are not
counted.<BR>
<b>Format of Data:</b>
<P>
<center>
<table border cellpadding=4 width=60%>
<caption align=bottom>
<B>HDF5 Back-Pointer Message Layout</B>
</caption>
<tr align=center>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<tr align=center>
<td colspan=4>Total Reference Count</td>
<tr align=center>
<td colspan=4>Dataset offset of Object #1</td>
<tr align=center>
<td colspan=4>Reference Count of Object #1</td>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
<tr align=center>
<td colspan=4>Dataset offset of Object #n</td>
<tr align=center>
<td colspan=4>Reference Count of Object #n</td>
</table>
</center>
<p>
<dl>
<dt>The elements of the back-pointer message are described below:
<dd>
<dl>
<dt>Total Reference Count: (32-bit unsigned integer)
<dd>This value stores the total number of times that the current dataset is
referenced by other objects within the file.
<dt>Dataset offset of Object: (<offset>-byte signed integer)
<dd>This is the dataset offset of an object in the current file which contains a pointer
to the current object.
<dt>Reference Count of Object: (32-bit unsigned integer)
<dd>This value stores the number of times that the dataset (above) references the
current object.
</dl>
</dl>
<h4><a name="BackPointerExample">Examples:</a></h4>
<dl>
<dt>Example #1
<dd>4 objects in an HDF file (Offsets: 1, 2, 3, 4) reference a fifth
object in the file (offset: 5) once each. The fifth object has a header message
containing a back-pointer message with the following information:
<pre>
Total Reference Count: 4
Offset of Object #1: 1
Reference Count of Object #1: 1
Offset of Object #2: 2
Reference Count of Object #2: 1
Offset of Object #3: 3
Reference Count of Object #3: 1
Offset of Object #4: 4
Reference Count of Object #4: 1
</pre>
<dt>Example #2
<dd>An object in an HDF file (offset: 1) references another object in the same
HDF file (offset: 10) fourteen times. A second object (offset: 4) references object
offset:10 seven times. Object offset:10 has the following back-pointer message:
<pre>
Total Reference Count: 21
Offset of Object #1: 1
Reference Count of Object #1: 14
Offset of Object #2: 4
Reference Count of Object #2: 7
</pre>
</dl>
-->
<hr>
<h3><a name="AttributeListMessage">Name: Attribute List</a></h3>
<b>Type:</b> 0x000C<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional, may be repeated.<BR>
<p><b>Purpose and Description:</b> The <em>Attribute List</em>
message is used to list objects in the HDF file which are used
as attributes, or "meta-data" about the current object. Other
objects can be used as attributes for either the entire object
or portions of the current object. The attribute list is
composed of two lists of objects, the first being simple
attributes about the entire dataset, and the second being
pointers attribute objects about the entire dataset. Partial
dataset pointers are currently unspecified and
unimplemented.
<p><b>Format of Data:</b>
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<b>HDF5 Attribute-List Message Layout</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>Attribute List Flags</td>
</tr>
<tr align=center>
<td colspan=4># of Simple Attributes</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Name Offset</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Data-Type</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Rank</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Dim #1 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Dim #2 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Dim #3 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Dim #4 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #1 Data Offset</td>
</tr>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Name Offset</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Data-Type</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Rank</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Dim #1 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Dim #2 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Dim #3 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Dim #4 Size</td>
</tr>
<tr align=center>
<td colspan=4>Simple Attribute #n Data Offset</td>
</tr>
<tr align=center>
<td colspan=4># of Complex Attributes</td>
</tr>
<tr align=center>
<td colspan=4>Pointer to Complex Attribute #1</td>
</tr>
<tr align=center>
<td colspan=4>.<br>.<br>.<br></td>
</tr>
<tr align=center>
<td colspan=4>Pointer to Complex Attribute #n</td>
</tr>
</table>
</center>
<p>
<dl>
<dt>The elements of the attribute list message are described below:
<dd>
<dl>
<dt>Attribute List Flags: (unsigned 32-bit integer)
<dd>These flags indicate the presence of simple and complex
lists of attributes for this dataset. Bit 0 indicates the
presence of a list of simple attributes and Bit 1
indicates the presence of a list of complex attributes.
<dt># of Simple Attributes: (unsigned 32-bit integer)
<dd>This indicates the number of simple attributes for this
dataset.
<dt>Simple Attribute #n Name Offset: (unsigned 32-bit integer)
<dd>This is the offset of the simple attribute's name in the
global small-data heap.
<dt>Simple Attribute #n Data-type: (unsigned 32-bit integer)
<dd>This is a simple data-type, which indicates the type of
data used for the attribute.
<dt>Simple Attribute #n Rank: (unsigned 32-bit integer)
<dd>This is the number of dimensions of the attribute,
limited to four or less.
<dt>Simple Attribute #n Dim #n Size: (unsigned 32-bit integer)
<dd>This is the size of the attribute's n'th dimension,
which is stored in the canonical order for dimensions
(i.e. no permutations of the indices are allowed).
<dt>Simple Attribute #n Data Offset: (unsigned 32-bit integer)
<dd>This is the offset of the simple attribute's data in the
global small-data.
<dt># of Complex Attributes: (unsigned 32-bit integer)
<dd>This indicates the number of complex attributes for this
dataset.
<dt>Pointer to Complex Attribute #n: (unsigned 32-bit integer)
<dd>This is the small-data heap offset of the name of the
attribute object in the file.
</dl>
</dl>
<p>[<b>Note:</b> It has been suggested that each attribute have an
additional "units" field, so this is being considered.]
<h4><a name="AttributeListExample">Examples:</a></h4>
[Comment: need examples.]
<hr>
<h3><a name="NameMessage">Name: Object Name</a></h3>
<b>Type:</b> 0x000D<BR>
<b>Length:</b> varies<BR>
<b>Status:</b> Optional [required?], may not be repeated.<BR>
<b>Purpose and Description:</b> The object name is designed to be a short
description of the instance of the data object (the class may be a short
description of the "type" of the object). An object name is a sequence of
non-zero ('\0') ASCII characters with no other formatting included by the
library.<BR>
<b>Format of Data:</b>The data for the object name is just a sequence of ASCII
characters with no special formatting.
<hr>
<h3><a name="ModifiedMessage">Name: Object Modification Date & Time</a></h3>
<b>Type:</b> 0x000E<BR>
<b>Length:</b> fixed<BR>
<b>Status:</b> Required?, may not be repeated.<BR>
<b>Purpose and Description:</b> The object modification date and time is a
timestamp which indicates (using ISO8601 date and time format) the last
modification of a data object.<BR>
<b>Format of Data:</b>
The date is represented as a fixed length ASCII string according to the
"complete calendar date representation, without hyphens" listed in the ISO8601
standard.<br>
The time of day is represented as a fixed length ASCII string according
to the "complete local time of day representation, without hyphens"
listed in the ISO8601 standard.
<h4><a name="ModifiedExample">Examples:</a></h4>
"February 14, 1993, 1:10pm and 30 seconds" is represented as "19930214131030" in
the ISO standard format.
<hr>
<h3><a name="SharedMessage">Name: Shared Object Message</a></h3>
<b>Type:</b> 0x000F<br>
<b>Length:</b> 4 Bytes<br>
<b>Status:</b> Optional, may be repeated.
<p>A constant message can be shared among several object headers
by writing that message in the global heap and having the object
headers all point to it. The pointing is accomplished with a
Shared Object message which is understood directly by the object
header layer of the library and never actually appears as a
message in the file. It is also possible to have a message of
one object header point to a message in some other object
header, but care must be exercised to prevent cycles.
<p>If a message is shared, then the message appears in the global
heap and its message ID appears in the Header Message Type
field of the object header. Also, the Flags field in the object
header for that message will have bit two set (the
<code>H5O_FLAG_SHARED</code> bit). The message body in the
object header will be that of a Shared Object message defined
here and not that of the pointed-to message.
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=top>
<b>Shared Message Message</b>
</caption>
<tr align=center>
<th width="25%">byte</td>
<th width="25%">byte</td>
<th width="25%">byte</td>
<th width="25%">byte</td>
</tr>
<tr align=center>
<td colspan=4>Flags</td>
</tr>
<tr align=center>
<td colspan=4><br>Pointer<br><br></td>
</tr>
</table>
</center>
<p>
<center>
<table align=center width="80%">
<tr>
<th width="30%">Field Name</th>
<th width="70%">Description</th>
</tr>
<tr valign=top>
<td>Flags</td>
<td>The Shared Message Message is a pointer to a Shared
Message. The actual shared message can appear in either
the global heap or in some other object header and this
field specifies which form is used. If the value is zero
then the actual message is the first such message in some
other object header; otherwise the actual message is
stored in the global heap.</td>
</tr>
<tr valign=top>
<td>Pointer</td>
<td>This field points to the actual message. The format of
the pointer depends on the value of the Flags field. If
the actual message is in the global heap then the pointer
is the file address of the global heap collection that
holds the message, and a four-byte index into that
collection. Otherwise the pointer is a symbol table entry
that points to some other object header.</td>
</tr>
</table>
</center>
<hr>
<h3><a name="ContinuationMessage">Name: Object Header Continuation</a></h3>
<b>Type:</b> 0x0010<BR>
<b>Length:</b> fixed<BR>
<b>Status:</b> Optional, may be repeated.<BR>
<b>Purpose and Description:</b> The object header continuation is the location
in the file of more header messages for the current data object. This can be
used when header blocks are large, or likely to change over time.<BR>
<b>Format of Data:</b><p>
The object header continuation is formatted as follows (assuming a 4-byte
length & offset are being used in the current file):
<P>
<center>
<table border cellpadding=4 width=60%>
<caption align=bottom>
<B>HDF5 Object Header Continuation Message Layout</B>
</caption>
<tr align=center>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<tr align=center>
<td colspan=4>Header Continuation Offset</td>
<tr align=center>
<td colspan=4>Header Continuation Length</td>
</table>
</center>
<P>
<dl>
<dt>The elements of the Header Continuation Message are described below:
<dd>
<dl>
<dt>Header Continuation Offset: (<offset> bytes)
<dd>This value is the offset in bytes from the beginning of the file where the
header continuation information is located.
<dt>Header Continuation Length: (<length> bytes)
<dd>This value is the length in bytes of the header continuation information in
the file.
</dl>
</dl>
<h4><a name="ContinuationExample">Examples:</a></h4>
[straightforward]
<hr>
<h3><a name="SymbolTableMessage">Name: Symbol Table Message</a></h3>
<b>Type:</b> 0x0011<BR>
<b>Length:</b> fixed<BR>
<b>Status:</b> Required for symbol tables, may not be repeated.<BR>
<b>Purpose and Description:</b> Each symbol table has a B-tree and a
name heap which are pointed to by this message.<BR>
<b>Format of data:</b>
<p>The symbol table message is formatted as follows:
<p>
<center>
<table border cellpadding=4 width="80%">
<caption align=bottom>
<b>HDF5 Object Header Symbol Table Message Layout</b>
</caption>
<tr align=center>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<th width="25%">byte</th>
<tr align=center>
<td colspan=4>B-Tree Address</td>
<tr align=center>
<td colspan=4>Heap Address</td>
</table>
</center>
<P>
<dl>
<dt>The elements of the Symbol Table Message are described below:
<dd>
<dl>
<dt>B-tree Address (<offset> bytes)
<dd>This value is the offset in bytes from the beginning of the file
where the B-tree is located.
<dt>Heap Address (<offset> bytes)
<dd>This value is the offset in bytes from the beginning of the file
where the symbol table name heap is located.
</dl>
</dl>
<h3><a name="SharedObjectHeader">Disk Format: Level 2b - Shared Data Object Headers</a></h3>
<P>In order to share header messages between several dataset objects, object
header messages may be placed into the global small-data heap. Since these
messages require additional information beyond the basic object header message
information, the format of the shared message is detailed below.
<BR> <BR>
<center>
<table border cellpadding=4 width=60%>
<caption align=bottom>
<B>HDF5 Shared Object Header Message</B>
</caption>
<tr align=center>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<th width=25%>byte</th>
<tr align=center>
<td colspan=4>Reference Count of Shared Header Message</td>
<tr align=center>
<td colspan=4><br> Shared Object Header Message<br> <br></td>
</table>
</center>
<p>
<dl>
<dt> The elements of the shared object header message are described below:
<dd>
<dl>
<dt>Reference Count of Shared Header Message: (32-bit unsigned integer)
<dd>This value is used to keep a count of the number of dataset objects which
refer to this message from their dataset headers. When this count reaches zero,
the shared message header may be removed from the global small-data heap.
<dt>Shared Object Header Message: (various lengths)
<dd>The data stored for the shared object header message is formatted in the
same way as the private object header messages described in the object header
description earlier in this document and begins with the header message Type.
</dl>
</dl>
<h3><a name="DataStorage">Disk Format: Level 2c - Data Object Data Storage</a></h3>
<P>The data information for an object is stored separately from the header
information in the file and may not actually be located in the HDF5 file
itself if the header indicates that the data is stored externally. The
information for each record in the object is stored according to the
dimensionality of the object (indicated in the dimensionality header message).
Multi-dimensional data is stored in C order [same as current scheme], i.e. the
"last" dimension changes fastest.
<P>Data whose elements are composed of simple number-types are stored in
native-endian IEEE format, unless they are specifically defined as being stored
in a different machine format with the architecture-type information from the
number-type header message. This means that each architecture will need to
[potentially] byte-swap data values into the internal representation for that
particular machine.
<P> Data with a "variable" sized number-type is stored in an data heap
internal to the HDF file [which should not be user-modifiable].
<P>Data whose elements are composed of pointer number-types are stored in several
different ways depending on the particular pointer type involved. Simple
pointers are just stored as the dataset offset of the object being pointed to with the
size of the pointer being the same number of bytes as offsets in the file.
Partial-object pointers are stored as a heap-ID which points to the following
information within the file-heap: an offset of the object pointed to, number-type
information (same format as header message), dimensionality information (same
format as header message), sub-set start and end information (i.e. a coordinate
location for each), and field start and end names (i.e. a [pointer to the]
string indicating the first field included and a [pointer to the] string name
for the last field).
Browse pointers are stored as an heap-ID (for the name in the file-heap)
followed by a offset of the data object being referenced.
<P>Data of a compound data-type is stored as a contiguous stream of the items
in the structure, with each item formatted according to it's
data-type.
<hr>
<address><a href="mailto:koziol@ncsa.uiuc.edu">Quincey Koziol</a></address>
<address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address>
<!-- hhmts start -->
Last modified: Mon Jun 1 21:44:38 EDT 1998
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